Installation in Linux HPC for use with the Lesion Quantification Toolkit

[William Drew]

Hello, I am trying to install dsi_studio on a linux (centos 7) HPC environment for use with the Lesion Quantification Toolkit (LQT). 

It appears that the LQT calls dsi_studio as an executable in a matlab script - what's the best way to obtain this executable? From the linux installation instructions it appears the only provided way to install dsi_studio is to launch it within a docker/singularity image. 

I don't have sudo on the compute cluster, so I don't think I'll be able to compile dsi_studio myself. Can someone help me to compile dsi_studio or is there another way to run dsi_studio as an executable?

Thanks, 

William

[Frank Yeh]

It seems to me that Docker or singularity would be the best solution
in your case.

It does not require sudo.

You only need to revise the code that calls DSI Studio with the
corresponding one to call Docker/singularity.

Best regards,
Frank

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[William Drew]

The problem I am running into is that Matlab is installed as a module on the cluster, which I do not know how to access from within the singularity. 'module load matlab' doesn’t work since environment variables aren’t the same. I’ve tried manually setting environment variables and mounting paths, but I am running into many problems with libraries. Is there a better solution?

Thanks,
William

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[Frank Yeh]

Are you able to run DSI Studio through singularity?

$ module load singularity
$ singularity pull docker://dsistudio/dsistudio
$ singularity exec dsistudio_latest.sif dsi_studio #GUI
$ singularity exec dsistudio_latest.sif dsi_studio --action=rec
--source=my.src.gz --thread_count=4 --method=7 --param0=1.7 #command
line

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[William Drew]

Yes, but I am unable to run the Matlab script inside the singularity container

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[Frank Yeh]

To get a disconnectivity matrix, all you need to do is to use lesion
as the ROI to run fiber tracking and generate a connectivity matrix.

It could be achieved in just one call to DSI Studio, for example.

dsi_studio --action=trk --source=subject_Data.fib.gz
--roi=lesion_in_subject_space.nii.gz --fiber_count=1000000
--connectivity=HCP_MMP

This will output a dis-connectivity matrix in MAT formats based on the lesion.
Is this what you are looking for?
Best,
Frank

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[Frank Yeh]

BTW, unless you want to process +1000 subject data.
The task could be easily done using a personal laptop with GUI.
HPC may be an overkill here IMHO.
Frank